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Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

From: "Crawford, Jeffrey" <>
To: Shilen Patel <>, "Redman, Chad" <>, "Hyzer, Chris" <>
Cc: " Mailing List" <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4
Date: Mon, 26 Nov 2018 18:54:33 +0000
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There was no drop constraint, the SQL command you provided didn’t work, I’ve been using:
SELECT * FROM grouper_pit_group_set WHERE owner_stem_id NOT IN (SELECT id FROM grouper_pit_stems);

I’ve only got two showing up in this environment, the same command is returning 0 rows in production, so we may be chasing an issue that’s only in our non-prod environment. Does that mean it’s safe to remove the two rows in grouper_pit_group_set that are dangling references?

I’ve only got ALTER TABLE … ADD CONSTRAINT and a few DROP TABLE … CASCADE CONSTRAINTS but no ALTER TABLE … DROP CONSTRAINT in the sql file.

Looking at our production it looks like we have the following constraints against the grouper_pit_group_set table:

fk_pit_gs_field_id

fk_pit_gs_member_attrdef_id

fk_pit_gs_member_field_id

fk_pit_gs_member_group_id

fk_pit_gs_member_stem_id

fk_pit_gs_owner_attrdef_id

fk_pit_gs_owner_group_id

fk_pit_gs_owner_stem_id

fk_pit_gs_parent_id

Does it look like any of the above is missing

Thanks for your help

Jeffrey Crawford

From: Shilen Patel <>
Date: Monday, November 26, 2018 at 10:18 AM
To: "Crawford, Jeffrey" <>, "Redman, Chad" <>, "Hyzer, Chris" <>
Cc: " Mailing List" <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

I believe that FK_PIT_GS_OWNER_STEM_ID constraint should have existed before you did the upgrade. Can you check if that’s the case or not? You’ll know by looking at your sql file (grouperDdl_20181120_10_28_37_190.sql) because if it did exist before the upgrade, then the sql file should have a statement that drops it towards the beginning.

If you determine that the constraint did not originally exist, then the way to make sure this doesn’t happen in production is by making sure it does exist before the upgrade (and of course fixing any issues that may be there when trying to add it).

If you determine that the constraint did exist, then it seems like the data somehow became inconsistent while the upgrade was running. It could be that the upgrade did something wrong. Or it could be that something else was modifying those point in time tables while the upgrade was happening.

For those 2 rows that you found in grouper_pit_group_set, is the active column set to T or F? If it’s F, it should be safe to delete.

Otherwise, does the following return anything (where the two params are the id values for the two rows in grouper_pit_group_set)?

select name from groups.grouper_stems where id in (

select owner_stem_id from groups.grouper_group_set where id in (

select source_id from groups.grouper_pit_group_set where id in (?, ?)

))

You can also run the pit sync script (if you’ve added all the views back) to get those tables corrected.

Thanks!

- Shilen

From: "Crawford, Jeffrey" <>
Date: Monday, November 26, 2018 at 11:00 AM
To: Shilen Patel <>, "Redman, Chad" <>, "Hyzer, Chris" <>
Cc: " Mailing List" <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

Morning Shilen,

Okay I reread your last message and missed that you gave me the columns and tables to check. I’ve come back with two in the grouper_pit_group_set that don’t match up with what’s in grouper_pit_stems. I guess my question is if it’s safe to remove the items in grouper_pit_group_set that don’t match. Or if that is just a signal for a larger problem that needs investigation.

Thanks

Jeffrey

From: <> on behalf of "Crawford, Jeffrey" <>
Date: Wednesday, November 21, 2018 at 1:21 PM
To: Shilen Patel <>, "Redman, Chad" <>, "Hyzer, Chris" <>
Cc: " Mailing List" <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

Humm, I’m wondering if the same problem might be present in our production side. I’m not usually in the database (Other than the audit table) Is there an easy way to check for the issue? That way I can run the same query in production.

Thanks

Jeffrey C.

From: Shilen Patel <>
Date: Wednesday, November 21, 2018 at 2:52 AM
To: "Crawford, Jeffrey" <>, "Redman, Chad" <>, "Hyzer, Chris" <>
Cc: " Mailing List" <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

Not necessarily. The upgrade sql script basically has the following steps:

1. Drop all views

2. Drop all foreign constraints

3. Upgrade the ddl

4. Set the new ddl version in the database

5. Add the foreign constraints

6. Add the views

Your original error (ORA-02298: cannot validate (IAMUCLA_GROUPER_D.FK_PIT_GS_OWNER_STEM_ID) - parent keys not found) probably happened during step 5 above.

You can now either run all the sql statements in the original sql script that didn’t run. Or do a “gsh -registry -deep” to get a new sql file with the missing ddl.

But before you do that, the original issue needs to be resolved. It seems like your point in time data is corrupt. If this is a dev environment and you don’t necessarily care about it, then you can truncate those tables. Otherwise, you’ll need to see why you have rows in grouper_pit_group_set with an owner_stem_id that’s not in grouper_pit_stems.

Alternatively, you could add the views back (from the sql script) which may be enough for you to start gsh at least. Then you can also run the pit sync script.

Thanks!

- Shilen

From: "Crawford, Jeffrey" <>
Date: Tuesday, November 20, 2018 at 5:44 PM
To: "Redman, Chad" <>, "Hyzer, Chris" <>, " Mailing List" <>, Shilen Patel <>
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

But wouldn't running gsh -registry -check correct that?

Get Outlook for Android

From: Shilen Patel <>
Sent: Tuesday, November 20, 2018 2:18:47 PM
To: Redman, Chad; Crawford, Jeffrey; Hyzer, Chris; Mailing List
Subject: Re: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

I'm guessing since the upgrade failed (the first error that was given), the views weren't added back (which usually happens at the end of the upgrade). So all these other errors may be a side effect.

- Shilen

Sent from my Verizon, Samsung Galaxy smartphone

-------- Original message --------

From: "Redman, Chad" <>

Date: 11/20/18 5:13 PM (GMT-05:00)

To: "Crawford, Jeffrey" <>, "Hyzer, Chris" <>, " Mailing List" <>

Subject: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

Syntax was almost right. Try this without the "as".

select ms.*, m.* from grouper_memberships_all_v ms, grouper_members m

where ms.owner_attr_def_id = '80075426c19b41758c65e6a6e74c6a9a'

and ms.member_id = '496458b5c1ca4757ab70541f15d3ec34'

and ms.member_id = m.id and ms.immediate_mship_enabled = 'T';

From: [mailto:] On Behalf Of Redman, Chad
Sent: Tuesday, November 20, 2018 5:09 PM
To: Crawford, Jeffrey <>; Hyzer, Chris <>; Mailing List <>
Subject: [grouper-users] RE: Trouble upgrading Grouper DB from 2.1 to 2.4

If it helps, this is the query the error translates to. Does this work from SQL? Logged in as iamucla_grouper_d?

/* edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO#findAllByGroupOwnerAndMember */

select ms.*, m.* from grouper_memberships_all_v as ms, grouper_members as m

where ms.owner_attr_def_id = '80075426c19b41758c65e6a6e74c6a9a'

and ms.member_id = '496458b5c1ca4757ab70541f15d3ec34'

and ms.member_id = m.id and ms.immediate_mship_enabled = 'T';

From: [] On Behalf Of Crawford, Jeffrey
Sent: Tuesday, November 20, 2018 2:41 PM
To: Hyzer, Chris <>; Mailing List <>
Subject: [grouper-users] Re: Trouble upgrading Grouper DB from 2.1 to 2.4

Maybe it’s just easier to post the errors I got:

./bin/gsh.sh

Using GROUPER_HOME: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF

Using GROUPER_CONF: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/classes

Using JAVA: /usr/java/jdk1.8.0_191-amd64/bin/java

using MEMORY: 64m-750m

log4j:WARN No such property [maxBackupIndex] in org.apache.log4j.DailyRollingFileAppender.

Grouper starting up: version: 2.4.0, build date: 2018/08/23 07:48:38, env: <no label configured>

grouperPatchStatus read from: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/grouperPatchStatus.properties

api patches installed: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9

ui patches installed: 0, 1, 2, 3, 4

grouper.properties read from: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/classes/grouper.properties

Grouper current directory is: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF

log4j.properties read from: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/classes/log4j.properties

Grouper is logging to file: /opt/grouper-2.4.0/apache-tomcat-8.5.12/logs/grouperUi/grouper_error.log, at min level WARN for package: edu.internet2.middleware.grouper, based on log4j.properties

grouper.hibernate.properties: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/classes/grouper.hibernate.properties

grouper.hibernate.properties:

subject.properties read from: /opt/grouper-2.4.0/grouper.ui-2.4.0/dist/grouper/WEB-INF/classes/subject.properties

sources configured in: subject.properties

subject.properties ldap source id: ldap: personLdap

subject.properties groupersource id: g:gsa

subject.properties groupersource id: grouperEntities

Grouper warning: cannot find group from config: deprovisioning admin group can deprovision from all groups/objects in Grouper even if the user is not a Grouper overall SysAdmin: etc:deprovisioning:deprovisioningAdmins

Grouper error: etc:deprovisioning:deprovisioningAdmins, edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in HibernateSession: HibernateSession (741741d0): notNew, notReadonly, READ_WRITE_NEW, activeTransaction, session (45a1d057),

Exception in list: (class [Ljava.lang.Object;), ByHqlStatic, query: 'select ms, m from MembershipEntry as ms, Member as m where ms.ownerGroupId = :owner and ms.memberUuid = :member and ms.memberUuid = m.uuid and ms.enabledDb = 'T'', cacheable: false, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'owner'->'8a101d8652034ff886576fd141f0cb70'Bind var[1]: 'Param (class java.lang.String): 'member'->'496458b5c1ca4757ab70541f15d3ec34', ,

Problem in HibernateSession: HibernateSession (1d98daa0): new, notReadonly, READ_WRITE_NEW, notActiveTransaction, session (45a1d057),

Problem saving group: etc:deprovisioning:deprovisioningAdmins, thread: 2d6e8792

at edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:589)

at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:711)

at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.list(ByHqlStatic.java:407)

at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.listSet(ByHqlStatic.java:458)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.findAllByGroupOwnerAndMember(Hib3MembershipDAO.java:1805)

at edu.internet2.middleware.grouper.privs.GrouperNonDbAccessAdapter.getPrivs(GrouperNonDbAccessAdapter.java:248)

at edu.internet2.middleware.grouper.privs.AccessWrapper.getPrivileges(AccessWrapper.java:139)

at edu.internet2.middleware.grouper.privs.GrouperAllAccessResolver.getPrivileges(GrouperAllAccessResolver.java:127)

at edu.internet2.middleware.grouper.privs.GrouperSystemAccessResolver.getPrivileges(GrouperSystemAccessResolver.java:109)

at edu.internet2.middleware.grouper.privs.CachingAccessResolver.getPrivileges(CachingAccessResolver.java:101)

at edu.internet2.middleware.grouper.privs.CachingAccessResolver.hasPrivilege(CachingAccessResolver.java:160)

at edu.internet2.middleware.grouper.privs.WheelAccessResolver.hasPrivilege(WheelAccessResolver.java:345)

at edu.internet2.middleware.grouper.privs.ValidatingAccessResolver.hasPrivilege(ValidatingAccessResolver.java:150)

at edu.internet2.middleware.grouper.Group.hasRead(Group.java:4525)

at edu.internet2.middleware.grouper.GroupSave$1$1.callback(GroupSave.java:642)

at edu.internet2.middleware.grouper.GrouperSession.callbackGrouperSession(GrouperSession.java:974)

at edu.internet2.middleware.grouper.GroupSave$1.callback(GroupSave.java:444)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3TransactionDAO$1.callback(Hib3TransactionDAO.java:66)

at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:701)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3TransactionDAO.transactionCallback(Hib3TransactionDAO.java:56)

at edu.internet2.middleware.grouper.hibernate.GrouperTransaction.callbackGrouperTransaction(GrouperTransaction.java:87)

at edu.internet2.middleware.grouper.hibernate.GrouperTransaction.callbackGrouperTransaction(GrouperTransaction.java:106)

at edu.internet2.middleware.grouper.GroupSave.save(GroupSave.java:435)

at edu.internet2.middleware.grouper.Group.saveGroup(Group.java:366)

at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroup(GrouperCheckConfig.java:221)

at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:853)

at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:499)

at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:315)

at edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell.java:165)

at edu.internet2.middleware.grouper.app.gsh.GrouperShellWrapper.main(GrouperShellWrapper.java:31)

Caused by: org.hibernate.exception.SQLGrammarException: could not extract ResultSet

at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:63)

at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)

at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109)

at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:95)

at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:79)

at org.hibernate.loader.Loader.getResultSet(Loader.java:2117)

at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1900)

at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1876)

at org.hibernate.loader.Loader.doQuery(Loader.java:919)

at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:336)

at org.hibernate.loader.Loader.doList(Loader.java:2617)

at org.hibernate.loader.Loader.doList(Loader.java:2600)

at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2429)

at org.hibernate.loader.Loader.list(Loader.java:2424)

at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:501)

at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:371)

at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:216)

at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1326)

at org.hibernate.internal.QueryImpl.list(QueryImpl.java:87)

at edu.internet2.middleware.grouper.hibernate.ByHql.list(ByHql.java:380)

at edu.internet2.middleware.grouper.hibernate.ByHqlStatic$2.callback(ByHqlStatic.java:417)

at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:701)

... 28 more

Caused by: java.sql.SQLSyntaxErrorException: ORA-00942: table or view does not exist

at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:459)

at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:400)

at oracle.jdbc.driver.T4C8Oall.processError(T4C8Oall.java:999)

at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:539)

at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:235)

at oracle.jdbc.driver.T4C8Oall.doOALL(T4C8Oall.java:543)

at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:239)

at oracle.jdbc.driver.T4CPreparedStatement.executeForDescribe(T4CPreparedStatement.java:1246)

at oracle.jdbc.driver.OracleStatement.executeMaybeDescribe(OracleStatement.java:1500)

at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1717)

at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:4401)

at oracle.jdbc.driver.OraclePreparedStatement.executeQuery(OraclePreparedStatement.java:4482)

at oracle.jdbc.driver.OraclePreparedStatementWrapper.executeQuery(OraclePreparedStatementWrapper.java:6272)

at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:353)

at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:70)

... 45 more

Couldnt startup grouper: Problem in HibernateSession: HibernateSession (7ce29a2d): notNew, notReadonly, READ_WRITE_NEW, activeTransaction, session (243bf087),

Exception in list: (class [Ljava.lang.Object;), ByHqlStatic, query: 'select ms, m from MembershipEntry as ms, Member as m where ms.ownerAttrDefId = :owner and ms.memberUuid = :member and ms.memberUuid = m.uuid and ms.enabledDb = 'T'', cacheable: false, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'owner'->'80075426c19b41758c65e6a6e74c6a9a'Bind var[1]: 'Param (class java.lang.String): 'member'->'496458b5c1ca4757ab70541f15d3ec34', ,

Problem in HibernateSession: HibernateSession (634ca3e7): new, notReadonly, READ_WRITE_NEW, notActiveTransaction, session (243bf087)

edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in HibernateSession: HibernateSession (7ce29a2d): notNew, notReadonly, READ_WRITE_NEW, activeTransaction, session (243bf087),

Problem in HibernateSession: HibernateSession (634ca3e7): new, notReadonly, READ_WRITE_NEW, notActiveTransaction, session (243bf087)

at edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:589)

at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:711)

at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.list(ByHqlStatic.java:407)

at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.listSet(ByHqlStatic.java:458)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.findAllByAttrDefOwnerAndMember(Hib3MembershipDAO.java:2542)

at edu.internet2.middleware.grouper.privs.GrouperNonDbAttrDefAdapter.getPrivs(GrouperNonDbAttrDefAdapter.java:194)

at edu.internet2.middleware.grouper.privs.AttributeDefWrapper.getPrivileges(AttributeDefWrapper.java:122)

at edu.internet2.middleware.grouper.privs.GrouperAllAttrDefResolver.getPrivileges(GrouperAllAttrDefResolver.java:99)

at edu.internet2.middleware.grouper.privs.GrouperSystemAttrDefResolver.getPrivileges(GrouperSystemAttrDefResolver.java:101)

at edu.internet2.middleware.grouper.privs.CachingAttrDefResolver.getPrivileges(CachingAttrDefResolver.java:133)

at edu.internet2.middleware.grouper.privs.CachingAttrDefResolver.hasPrivilege(CachingAttrDefResolver.java:201)

at edu.internet2.middleware.grouper.privs.WheelAttrDefResolver.hasPrivilege(WheelAttrDefResolver.java:341)

at edu.internet2.middleware.grouper.privs.ValidatingAttrDefResolver.hasPrivilege(ValidatingAttrDefResolver.java:127)

at edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate.hasAttrAdmin(AttributeDefPrivilegeDelegate.java:87)

at edu.internet2.middleware.grouper.attr.AttributeDefSave$1$1.callback(AttributeDefSave.java:738)

at edu.internet2.middleware.grouper.GrouperSession.callbackGrouperSession(GrouperSession.java:974)

at edu.internet2.middleware.grouper.attr.AttributeDefSave$1.callback(AttributeDefSave.java:495)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3TransactionDAO$1.callback(Hib3TransactionDAO.java:66)

at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:701)

at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3TransactionDAO.transactionCallback(Hib3TransactionDAO.java:56)

at edu.internet2.middleware.grouper.hibernate.GrouperTransaction.callbackGrouperTransaction(GrouperTransaction.java:87)

at edu.internet2.middleware.grouper.hibernate.GrouperTransaction.callbackGrouperTransaction(GrouperTransaction.java:106)

at edu.internet2.middleware.grouper.attr.AttributeDefSave.save(AttributeDefSave.java:488)

at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttributes(GrouperCheckConfig.java:2080)

at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:501)